align_reads: Align Reads

In selkamand/utilitybeltrefseq: What the Package Does (One Line, Title Case)

Align Reads

Description

Align Reads

Usage

align_reads(
  bwa_index_prefix,
  forward_reads,
  reverse_reads,
  outfile_prefix,
  bwa_options = "",
  threads = parallel::detectCores()
)

Arguments

bwa_index_prefix	prefix of indexed reference genome (e.g. output of prep_for_alignment()) (string)
forward_reads	path to fastq file containing forward reads (string)
reverse_reads	path to fastq file containing reverse reads (string)
outfile_prefix	prefix used for output alignment files
bwa_options	supply any other options to bwa-mem2 mem command. For example '-k 50' will change min seed length to 50. (string)
threads	how many cup threads to use (int)

Value

outfile path

Examples

## Not run: 

prep_for_alignment()

## End(Not run)

selkamand/utilitybeltrefseq documentation built on July 7, 2022, 7:35 a.m.